I am trying to simulate a nanocomposite using Silica as the nanoparticle and nylon6 as the polymer. When I try to construct the model using the amorphous cell construction module, the resulting cell has intersection between the nylon chains and the Silica particle. I have used various display styles to make sure that there is intersection and that it is not an optical illusion. There are some bons between the nylon chains and the Silica particle. Is there a bug in the new version or am I making a mistake?

Any help in this matter will be apprecaited.

Thank you